Align Histidine transport ATP-binding protein HisP (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= SwissProt::P02915 (258 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 147 bits (370), Expect = 5e-40 Identities = 85/238 (35%), Positives = 143/238 (60%), Gaps = 18/238 (7%) Query: 22 LKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINLVRDKDGQLK 81 ++ S + G++ I+G SGSGKST +R +N L +P+ G ++++G++I V D QL Sbjct: 46 VQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDI--VAMNDDQL- 102 Query: 82 VADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERALKYLAKVG 141 +++ R +L+MVFQ F L HMTVL+N +++ G+ K +RAL+ L +VG Sbjct: 103 ------VKVRRAKLSMVFQSFALMPHMTVLQNAAFG-LEMDGVDKQTREQRALQALEQVG 155 Query: 142 IDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDP----ELVGEVLRIMQ 197 ++ A+ P LSGG QQRV +AR LA++PD+LL DE SALDP E+ E+L++ Sbjct: 156 LEAWAESM-PDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQ- 213 Query: 198 QLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFLKG 255 A+ +T+V ++H++ A + + + G++ + G PE++ NP ++ F +G Sbjct: 214 --AKAKRTIVFISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRG 269 Lambda K H 0.319 0.136 0.383 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 258 Number of extensions: 13 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 258 Length of database: 415 Length adjustment: 28 Effective length of query: 230 Effective length of database: 387 Effective search space: 89010 Effective search space used: 89010 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory